Proteomics studies of the interactome of RNA polymerase II C-terminal repeated domain

Pineda, Gabriel; Shen, Zhouxin; de Albuquerque, Claudio Ponte; Reynoso, Eduardo; Chen, Jeffrey; Tu, Chi-Chiang; Tang, Wingchung; Briggs, Steve; Zhou, Huilin; Wang, Jean Y. J.

doi:10.1186/s13104-015-1569-y

BMC Research Notes

Table 1 Proteins Identified by the MUDPIT analyses of CTD-peptide pull-down fractions

From: Proteomics studies of the interactome of RNA polymerase II C-terminal repeated domain

Gene symbol	IPI accession number	Percent coverage (%)	Unique peptide	Score	CTD	tyr1	ser2	ser5	ser2tyr1	ser5tyr1
ESYT2	IPI00409635	38	25	423.67	0	0	0	0	46	104
ESYT1	IPI00022143	39	31	497.94	0	0	0	0	43	96
PLD1	IPI00218797	29	25	370.49	0	0	0	0	17	52
HSP90B1	IPI00027230	24	17	254.42	2	0	0	8	5	50
HSPE1	IPI00220362	67	10	134.68	3	1	0	7	3	41
CANX	IPI00020984	23	14	196.91	0	0	3	0	0	38
PDIA6	IPI00299571	24	9	151.87	0	0	0	4	4	34
TRAP1	IPI00030275	14	8	134.8	0	0	0	5	0	29
PDIA3	IPI00025252	30	12	176.8	0	0	0	4	2	23
P4HB	IPI00010796	24	11	157.3	1	0	0	2	1	22
ATP1A1	IPI00006482	13	11	161.54	0	0	0	1	0	19
RPL4	IPI00003918	16	6	96.02	1	0	7	0	0	19
GAPDH	IPI00219018	24	7	103.11	2	0	0	3	6	17
TUFM	IPI00027107	20	7	109.33	0	0	0	0	1	16
RPN1	IPI00025874	19	10	117.2	0	0	2	0	0	15
LRRC59	IPI00396321	28	7	101.92	0	0	0	0	2	15
SFPQ	IPI00010740	11	6	83.98	2	0	0	4	1	15
DDX21**	IPI00015953	17	13	174.19	0	0	5	0	0	14
LMNA	IPI00021405	16	10	138.09	0	0	0	1	0	14
ATP5B	IPI00303476	16	6	97.21	0	0	0	0	3	13
KHSRP	IPI00479786	18	9	129.15	0	0	0	2	0	12
TUBB	IPI00011654	10	3	51.99	0	0	0	0	1	12
CALR	IPI00020599	31	9	123.08	0	0	0	2	1	11
ALDOA	IPI00796333	20	5	85.11	0	0	0	2	3	11
RAB7A	IPI00016342	26	5	80.8	0	0	0	3	0	11
ATP5A1	IPI00440493	14	7	96.43	0	0	0	2	2	10
RCN1	IPI00015842	28	7	90.96	0	0	0	0	2	10
TKT	IPI00788802	12	6	84.06	1	0	0	0	0	10
RPN2	IPI00028635	10	4	61.66	1	0	0	0	0	10
RPL7A	IPI00479315	23	7	97.03	0	0	3	0	0	9
HNRPU	IPI00644079	10	7	95.98	0	0	2	0	1	9
SERBP1	IPI00410693	15	5	79.22	0	0	0	1	1	9
SLC25A5	IPI00007188	17	5	68.2	0	0	0	0	1	9
RTN4	IPI00021766	2	3	50.99	0	0	1	1	0	9
HNRPC**	IPI00477313	26	8	111.38	0	0	5	0	0	8
VIM	IPI00418471	21	9	110.44	0	0	0	0	2	8
NONO	IPI00304596	16	8	98.5	0	0	0	5	0	8
ANXA2	IPI00418169	24	6	93.12	0	0	0	0	1	8
MATR3	IPI00789551	12	7	92.94	0	0	2	0	0	8
DDX5**	IPI00017617	9	6	79.42	0	0	3	0	0	8
PPIB	IPI00646304	25	6	69.98	0	0	0	2	0	8
RPL18	IPI00215719	21	4	54.14	0	0	4	0	0	8
RPL6	IPI00790342	26	7	105.24	0	0	7	0	0	7
CROP	IPI00107745	11	3	52.2	0	0	0	0	4	7
RAB1A	IPI00005719	18	3	45.79	0	0	0	2	1	7
PRKCSH	IPI00026154	8	3	53.39	0	0	0	1	0	6
RPRD2	IPI00384541	34	38	543.2	0	0	63	0	20	5
PHF3	IPI00170770	17	28	411.08	0	0	13	0	83	5
HNRNPUL2	IPI00456887	7	5	67.71	0	0	0	0	3	5
RPL7	IPI00472171	13	4	56.17	0	0	3	0	0	5
RPL29	IPI00796934	15	3	44.49	0	0	1	0	1	5
KIAA1429	IPI00036742	10	17	253.56	0	0	14	0	13	4
ZC3H13	IPI00329547	7	12	154.87	0	0	7	0	5	4
WTAP	IPI00220302	25	8	120	0	0	4	0	3	4
RBMX**	IPI00304692	15	6	75.41	0	0	6	0	0	4
HNRPD	IPI00028888	8	3	42.87	0	0	0	1	0	4
TMPO	IPI00216230	6	3	40.25	0	0	0	1	0	4
SSBP1	IPI00029744	22	2	32.28	0	0	0	2	0	4
SFRS3	IPI00010204	14	2	28.23	0	0	0	0	0	4
RBM15**	IPI00102752	18	16	217.62	0	0	21	0	9	3
NPM1	IPI00549248	17	4	60.16	1	0	1	0	1	3
RPL8	IPI00797230	14	4	52.41	2	0	4	0	0	3
RPL23A	IPI00789159	16	3	46.69	0	0	3	0	0	3
RPL15	IPI00375511	16	4	46.24	0	0	10	0	0	3
RPL28	IPI00182533	18	3	37.93	0	0	3	0	0	3
LOC654188	IPI00419585	16	3	34.68	0	0	0	1	0	3
RPL35	IPI00412607	15	2	31.35	0	0	4	0	0	3
RPS14	IPI00026271	15	2	30.42	1	0	0	0	0	3
hCG_2040224	IPI00412855	13	2	27.87	0	0	2	0	0	3
DST	IPI00074148	0	2	25.88	2	1	0	1	1	3
RPRD1B	IPI00009659	24	8	121.65	0	0	40	0	6	2
RPS9	IPI00221088	20	4	51.03	0	0	2	0	0	2
HNRNPH1	IPI00479191	12	4	50.57	0	0	0	2	0	2
RPL26	IPI00433834	11	3	35.94	0	0	3	0	0	2
SUMO2	IPI00299149	23	2	31.08	0	0	0	1	0	2
HNRPM**	IPI00171903	5	4	49.84	0	0	3	0	0	1
LOC641293	IPI00845507	18	3	38.98	0	0	3	0	0	1
RPL31	IPI00848331	25	3	35.4	0	0	2	0	0	1
PRSS1	IPI00011694	9	3	34.11	10	39	0	5	13	1
SF3A1	IPI00017451	4	2	31.33	1	0	0	0	0	1
RPL10	IPI00646899	8	2	30.62	0	0	7	0	0	1
AOC3	IPI00004457	1	2	26.37	0	0	0	3	1	1
LOC730004	IPI00787417	23	2	24.8	1	0	0	0	0	1
TMPRSS13	IPI00000848	3	2	24.18	10	36	0	4	14	1
LACTB	IPI00749059	24	10	145.3	0	0	0	0	15	0
SCAF8	IPI00744707	7	9	107.99	0	0	17	0	0	0
SCAF4	IPI00181702	6	7	82.65	0	0	12	0	1	0
RNGTT	IPI00000104	7	4	58.94	0	0	0	11	0	0
GC	IPI00555812	9	3	43.86	3	0	0	0	0	0
DSP	IPI00013933	1	3	42.82	3	0	0	0	0	0
FKBP15	IPI00401282	2	3	36.89	0	0	0	0	5	0
CBLL1	IPI00290429	5	2	34.71	0	0	4	0	0	0
HNRNPUL1**	IPI00013070	3	3	32.92	0	0	8	0	0	0
MGAM	IPI00220143	1	2	27.01	0	0	0	2	0	0
STOML2	IPI00334190	8	2	23.18	0	0	0	0	2	0
KIAA1881	IPI00787298	1	2	22.61	0	0	0	2	0	0
PRPF6	IPI00305068	1	2	22.54	2	0	0	0	0	0
DIDO1	IPI00619921	1	2	22.43	0	0	0	0	2	0
DSG1	IPI00025753	2	2	22.18	2	0	0	0	0	0
DSC1	IPI00216099	3	2	20.02	2	0	0	0	0	0

Lists the proteins that were identified from peptide pull-down using differentially phosphorylated CTD peptides. The official gene symbol and accession number are listed in the first two columns. Percent coverage column shows the percentage of the protein’s sequence represented by the peptides identified in the MS/MS analysis. Unique peptides column shows total number of peptides that were identified. Score: score from Spectrum Mill. The other columns show the total number of peptides identified in each of the indicated pull-down fractions with beads alone (no peptide), and each of the six CTD peptides illustrated in Fig. 1a. Proteins marked by ** were those identified in two independent experiments by (a) MS/MS identification of gel bands in the pull-down fractions and (b) MUDPIT identification of the entire pull-down fractions. The four CID-containing proteins are highlighted in italics. Note that the MUDPIT experiment identified more proteins, which are listed here

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ISSN: 1756-0500

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